NovelTree is a highly parallelized and computationally efficient phylogenomic workflow that infers gene families, gene family trees, species trees, and gene family evolutionary history.
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Monophyly constraints for gene tree and/or species tree inference #21
Create option to provide a list of monophyly constraints to expedite gene family tree and (possibly) species tree inference.
For gene family trees, this will likely mean a list of species per group for which we confidently expect there to be no legitimate reason for HGT/hybridization with other groups - e.g. at the level of taxonomic supergroup, or enforcing monophyly for euks and archaea respectively.
Internally will need to correspond sequence names (Genus_species:SeqID) to species names, since this will entail monophyly of species, each with (potentially) multiple gene copies.
Description of feature
Create option to provide a list of monophyly constraints to expedite gene family tree and (possibly) species tree inference.
For gene family trees, this will likely mean a list of species per group for which we confidently expect there to be no legitimate reason for HGT/hybridization with other groups - e.g. at the level of taxonomic supergroup, or enforcing monophyly for euks and archaea respectively.
Internally will need to correspond sequence names (Genus_species:SeqID) to species names, since this will entail monophyly of species, each with (potentially) multiple gene copies.